TCGAanalyze_Filtering: Filtering mRNA transcripts and miRNA selecting a threshold.

Description Usage Arguments Value Examples

View source: R/analyze.R

Description

TCGAanalyze_Filtering allows user to filter mRNA transcripts and miRNA, samples, higher than the threshold defined quantile mean across all samples.

Usage

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TCGAanalyze_Filtering(
  tabDF,
  method,
  qnt.cut = 0.25,
  var.func = IQR,
  var.cutoff = 0.75,
  eta = 0.05,
  foldChange = 1
)

Arguments

tabDF

is a dataframe or numeric matrix, each row represents a gene, each column represents a sample come from TCGAPrepare

method

is method of filtering such as 'quantile', 'varFilter', 'filter1', 'filter2'

qnt.cut

is threshold selected as mean for filtering

var.func

is function used as the per-feature filtering statistic. See genefilter documentation

var.cutoff

is a numeric value. See genefilter documentation

eta

is a parameter for filter1. default eta = 0.05.

foldChange

is a parameter for filter2. default foldChange = 1.

Value

A filtered dataframe or numeric matrix where each row represents a gene, each column represents a sample

Examples

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dataNorm <- TCGAbiolinks::TCGAanalyze_Normalization(dataBRCA, geneInfo)
dataNorm <- TCGAanalyze_Normalization(tabDF = dataBRCA,
geneInfo = geneInfo,
method = "geneLength")
dataFilt <- TCGAanalyze_Filtering(tabDF = dataNorm, method = "quantile", qnt.cut = 0.25)

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.